Wrong rendering order of particles, hitboxes, clouds, transparent blocks, breaking animations and various other transparent textures

Affected cases

1. Some particles render behind transparent blocks, hitboxes, breaking animations and transparent clouds, often making them barely visible. Particles known to have this issue: End rod, potion, fireowork, ink, rain and snow particles. In older versions, this was a general issue with all types of particles, some have been fixed since then.
2. As of 13w41a, hitboxes render in front of transparent blocks - it simply looks weird when you can see the hitbox of blocks through the water surface (see water_hitbox.jpg) or the rear (normally less visible) parts of the hitbox through a transparent block like ice or stained glass. As of 1.7, the behavior changed: Hitboxes now render behind transparent blocks!
3. Transparent clouds ¹ always render in front of transparent blocks and hitboxes (looks pretty weird, see clouds_glass.jpg).
4. The energy field around invisible charged creepers renders behind water and transparent clouds, but in front of hitboxes. Particles and other transparent blocks show no rendering order problems in this case. You can spawn invisible charged creepers with the following command:

   /summon creeper ~ ~1 ~ {powered:1b,ActiveEffects:[{Id:14,Duration:2000000}]}
   

1. The firework explosion light flash causes water and transparent clouds to always be rendered behind it, making them disappear.
2. The outer, transparent part of the beacon beam, the transparent text overlay of named map markers (close to a map's edge) as well as the outer transparent part of Phantom wings render behind water, transparent clouds and transparent blocks, making them disappear.
3. Ice blocks render incorrectly in third person

Notes

¹ "Transparent clouds" means: Clouds turn transparent when you move above y=128 (MC-997). Before Jeb reverted the fix of MC-997, clouds were always transparent at all heights, which can be seen here 2013-02-27_21.46.57.png)

Code analysis

See this comment.

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^{Mod edit: Added comment by Tedstar (Curtis Anderson)}

Some updates from snapshot 18w22a (and possibly earlier)

Issues resolved in snapshot 18w22a:

• Hitboxes now render underwater and through water.
• Non-transparent particles render correctly in front of transparent blocks (ex breaking stone in front of water).

Issues new to 18w22a:

• Hitboxes render completely behind transparent blocks (ice, colored glass) making them hard to see.

Issues still present in 18w22a:

• Beacon beam outer aura renders behind transparent blocks at any height.
• Transparent particles render in place of transparent blocks. (Ex: break stained glass in front of ocean, squid ink looking upward in water, etc.)
• Charged creeper aura renders in place of transparency (water, ice, etc.)
• Phantom wings render in place of transparency.
• Ice still renders strangely at far distances.
• Clouds still render in front of transparent blocks/water when placed above the cloud height.
• Firework particles still render in behind transparent blocks.

I'm sure I forgot many of them, but these are the ones that are easily noticed to me.